EDS have probably devised their maps based on tuning hundreds, if not thousands of Z20LEx powered cars, so I would think it'd be safe to assume they've got a tune that would suit whatever mods you have, as they've probably seen every combination there is. I would say a custom tune would only be worth looking at when you go past stage 3.5, as that's when you'd yield the most from any form of custom tune (and start venturing into the more exclusive and unknown territories). Other than that, the EDS IPF is more than sufficient for what you need now.
Yes, there are many different types and variants of intercoolers, exhausts, etc on the market, the power differences for example between say a TX intercooler and an Airtec branded intercooler are probably not enough to warrant a custom tune (Although the Airtec cooler looks better in comparison and would be of far better build quality).